{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS3005LSBM/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3005LSBM",
"aliases": [
"ansuman-satpathy:igvf12_analysis_set_10x3"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0049EKWC](/matrix-files/IGVFFI0049EKWC/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0049EKWC/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0049EKWC](/matrix-files/IGVFFI0049EKWC/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0049EKWC/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS3005LSBM](/analysis-sets/IGVFDS3005LSBM/) has `input_file_sets` with multiplexed samples: [IGVFSM7114MTSH](/multiplexed-samples/IGVFSM7114MTSH/) but no `demultiplexed_sample`. Analysis sets with multiplexed samples are expected to specify a demultiplexed sample.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_analysis_set_multiplexed_samples",
"path": "/analysis-sets/IGVFDS3005LSBM/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS3005LSBM](/analysis-sets/IGVFDS3005LSBM/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/analysis-sets/IGVFDS3005LSBM/"
},
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM7114MTSH](/multiplexed-samples/IGVFSM7114MTSH/) has in progress subobject tabular file [IGVFFI6870GMPP](/tabular-files/IGVFFI6870GMPP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM7114MTSH/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM7114MTSH](/multiplexed-samples/IGVFSM7114MTSH/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/multiplexed-samples/IGVFSM7114MTSH/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"controlled_access": true,
"creation_timestamp": "2025-03-21T23:04:53.143037+00:00",
"data_use_limitation_summaries": [
"GRU"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"aliases": [
"ansuman-satpathy:singh_bcell_donor_2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"aliases": [
"ansuman-satpathy:singh_bcell_donor_1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1264SGCS/",
"accession": "IGVFDO1264SGCS",
"aliases": [
"ansuman-satpathy:bridge_bone_marrow_donor_2038"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI0049EKWC/",
"accession": "IGVFFI0049EKWC",
"aliases": [
"ansuman-satpathy:igvf12_raw_rna_counts_10x3"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:07:46.553005+00:00",
"file_format": "hdf5",
"file_size": 179198907,
"href": "/matrix-files/IGVFFI0049EKWC/@@download/IGVFFI0049EKWC.h5",
"s3_uri": "s3://igvf-files/2025/01/28/0699b023-8e8f-4cf3-90f6-d738b0167a7e/IGVFFI0049EKWC.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l3_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI0803IASQ/",
"accession": "IGVFFI0803IASQ",
"aliases": [
"ansuman-satpathy:igvf12_fragments_index_10x3"
],
"content_type": "index",
"controlled_access": true,
"creation_timestamp": "2025-01-28T15:28:44.981305+00:00",
"file_format": "tbi",
"file_size": 1697457,
"href": "/index-files/IGVFFI0803IASQ/@@download/IGVFFI0803IASQ.tbi",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/0ed33217-ce43-455d-ae45-59fe1b5d97b6/IGVFFI0803IASQ.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l3_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI3429KVCC/",
"accession": "IGVFFI3429KVCC",
"aliases": [
"ansuman-satpathy:igvf12_multiseq_count_matrix_10x3"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:33:44.256689+00:00",
"file_format": "tsv",
"file_size": 107329,
"href": "/tabular-files/IGVFFI3429KVCC/@@download/IGVFFI3429KVCC.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/efc37389-f375-4c80-863f-39a822666f15/IGVFFI3429KVCC.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e12l3_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI9846AWHA/",
"accession": "IGVFFI9846AWHA",
"aliases": [
"ansuman-satpathy:igvf12_peaks_10x3"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:14:17.619860+00:00",
"file_format": "bed",
"file_size": 1199916,
"href": "/tabular-files/IGVFFI9846AWHA/@@download/IGVFFI9846AWHA.bed.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/0d23b10e-136c-4a43-8ed7-8584a3ac1317/IGVFFI9846AWHA.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l3_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI3421TIBT/",
"accession": "IGVFFI3421TIBT",
"aliases": [
"ansuman-satpathy:igvf12_fragments_10x3"
],
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:13:22.665178+00:00",
"file_format": "tsv",
"file_size": 5172584411,
"href": "/tabular-files/IGVFFI3421TIBT/@@download/IGVFFI3421TIBT.tsv.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/5e1a25da-e55d-4017-9d7c-f490c199b27f/IGVFFI3421TIBT.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l3_fragments.tsv.gz",
"upload_status": "validation exempted"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5862OZVJ/",
"accession": "IGVFDS5862OZVJ",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf12_10x3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8054AFXK/",
"accession": "IGVFDS8054AFXK",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf12_10x3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS8701GVWQ/",
"accession": "IGVFDS8701GVWQ",
"aliases": [
"ansuman-satpathy:multiseq_igvf12_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"release_timestamp": "2025-03-22T00:43:16.836542+00:00",
"sample_summary": "Homo sapiens multiplexed sample of B cell, bone marrow",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7114MTSH/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7114MTSH",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf12_10x3"
],
"classifications": [
"differentiated cell specimen",
"tissue",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/1e03eda3-a983-4cee-864e-43acb4c1b186/",
"certificate_identifier": "IP115-18",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
},
{
"@id": "/institutional-certificates/460c2060-3b32-43c1-ab4b-b2ef0fbeb2b2/",
"certificate_identifier": "IP115-22",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "B cell",
"term_name": "B cell"
},
{
"@id": "/sample-terms/UBERON_0002371/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "bone marrow",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/6667a92a-d202-493a-8c7d-7a56d1380356/",
"title": "Khine Lin"
},
"submitted_files_timestamp": "2025-01-28T06:13:22.665178+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "4a3bf2c8-ce92-4d5f-b367-f7dc6e64b5f6",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}